Huge Emergency 9:30 at night...HELP!!

I had a bad storm last night, but had water this morning. It was hot, but running rusty color. Tonight, I noticed rust color in the toilet. I ran all the faucets (rust and mud coming out) and then water stopped running. I noticed a pulsing noise from the crawl space which only stopped when I shut the electric off (the circuits that say sump pump and water). The noise isn't coming from the sump pump. The hot water heater is in the broom closet, but there is another big blue tank in the crawl space / basement. That's where the noise is coming from.

I have a well and holding tanks. I'm a new home owner and don't know what I'm doing. Is there any chance that this will all be better in the morning? If not, what do you think it is. I'd appreciate some quick answers. I think I'm in real trouble here.

The air bladder in that blue pressure tank may be leaking. If it is, you will have to replace it.
Check it with the air valve on top. If water blows out of that air valve, the bladder is definitely shot.
If water does NOT shoot out of the air valve -- with the power to the pump OFF and the water pressure drained down -- check the air pressure with a tire gauge. It should be two PSI below your pump cut-on pressure (e.g. if the pump is set at 30-50 cut-on/cut-off, it should be 28 psi).
If it needs air, air it up with a bicycle pump or portable air tank or compressor.
The storm may have flooded the top of your well head, and it may just clear itself up.
If you keep having problems, you need to call a well-and-pump man or a plumber experienced at working on them.
Good luck!
Mike